Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

CORC > 水生生物研究所 > 中科院水生所知识产出（2009年前） > 水生生物分子与细胞生物学研究中心 > 期刊论文

	Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing
	Xiong, Jie 1,5; Lu, Xingyi 1,5; Zhou, Zhemin 2; Chang, Yue 1,5; Yuan, Dongxia 1; Tian, Miao 1,5; Zhou, Zhigang 4; Wang, Lei 2; Fu, Chengjie 1; Orias, Eduardo 3
刊名	PLOS ONE
	2012-02-07
卷号	7 期号:2 页码:e30630
关键词	PROGRAMMED DNA ELIMINATION ACTIVATED PROTEIN-KINASE GENOME-WIDE ANALYSIS GENE-EXPRESSION FUNCTIONAL GENOMICS CANDIDA-ALBICANS SPLICE JUNCTIONS SEQ ANNOTATION YEAST
ISSN号	1932-6203
通讯作者	Xiong, J (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China.
中文摘要	Background: The ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation. Methodology/Principal Findings: This RNA-seq study describes the first deep sequencing analysis of the T. thermophila transcriptome during the three major stages of the life cycle: growth, starvation and conjugation. Uniquely mapped reads covered more than 96% of the 24,725 predicted gene models in the somatic genome. More than 1,000 new transcribed regions were identified. The great dynamic range of RNA-seq allowed detection of a nearly six order-of-magnitude range of measurable gene expression orchestrated by this cell. RNA-seq also allowed the first prediction of transcript untranslated regions (UTRs) and an updated (larger) size estimate of the T. thermophila transcriptome: 57 Mb, or about 55% of the somatic genome. Our study identified nearly 1,500 alternative splicing (AS) events distributed over 5.2% of T. thermophila genes. This percentage represents a two order-of-magnitude increase over previous EST-based estimates in Tetrahymena. Evidence of stage-specific regulation of alternative splicing was also obtained. Finally, our study allowed us to completely confirm about 26.8% of the genes originally predicted by the gene finder, to correct coding sequence boundaries and intron-exon junctions for about a third, and to reassign microarray probes and correct earlier microarray data. Conclusions/Significance: RNA-seq data significantly improve the genome annotation and provide a fully comprehensive view of the global transcriptome of T. thermophila. To our knowledge, 5.2% of T. thermophila genes with AS is the highest percentage of genes showing AS reported in a unicellular eukaryote. Tetrahymena thus becomes an excellent unicellular model eukaryote in which to investigate mechanisms of alternative splicing.
英文摘要	Background: The ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation.
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	PROGRAMMED DNA ELIMINATION ; ACTIVATED PROTEIN-KINASE ; GENOME-WIDE ANALYSIS ; GENE-EXPRESSION ; FUNCTIONAL GENOMICS ; CANDIDA-ALBICANS ; SPLICE JUNCTIONS ; SEQ ; ANNOTATION ; YEAST
收录类别	SCI
资助信息	Chinese Academy of Sciences[KSCX2-EW-G-6-4]; National Natural Science Foundation of China[Y11314-1-501, Y01307-1-501]; National Science Foundation, United States of America[MCB-1025069]
语种	英语
WOS记录号	WOS:000302180600012
公开日期	2012-09-25
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/17021]
专题	水生生物研究所_水生生物分子与细胞生物学研究中心_期刊论文
作者单位	1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China 2.Nankai Univ, Tianjin Econ Technol Dev Area, Sch Biol Sci & Biotechnol, Tianjin 300071, Peoples R China 3.Univ Calif Santa Barbara, Dept Mol Cellular & Dev Biol, Santa Barbara, CA 93106 USA 4.Chinese Acad Agr Sci, Feed Res Inst, Beijing 100193, Peoples R China 5.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Xiong, Jie,Lu, Xingyi,Zhou, Zhemin,et al. Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing[J]. PLOS ONE,2012,7(2):e30630.
APA	Xiong, Jie.,Lu, Xingyi.,Zhou, Zhemin.,Chang, Yue.,Yuan, Dongxia.,...&Miao, Wei.(2012).Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing.PLOS ONE,7(2),e30630.
MLA	Xiong, Jie,et al."Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing".PLOS ONE 7.2(2012):e30630.